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Series GSE9234 Query DataSets for GSE9234
Status Public on Mar 01, 2008
Title Correlation of microRNA levels during hypoxia with predicted target mRNAs through genome-wide microarray analysis
Platform organisms Homo sapiens; Mus musculus; Rattus norvegicus
Sample organism Homo sapiens
Experiment type Expression profiling by array
Non-coding RNA profiling by array
Summary three replicates of HT29 cells per conditionwere grown under normoxic and hypoxic conditions. RNA and miRNA was extracted from each replicate and run on the GPL570 and GPL5106 arrays respectively.
Low levels of oxygen in tissues, seen in situations such as chronic lung disease, necrotic tumors, and high altitude exposures, initiate a signaling pathway that results in active transcription of genes possessing a hypoxia response element (HRE). To identify changes induced by hypoxia and determine whether miRNA may have effects on gene expression, we conducted mRNA- and miRNA-array-based analysis on HT29 cells, and developed methods for the comparative analysis of these data sets. To date, no studies have examined the effects of an environmental perturbation on miRNA levels and their relationship to gene expression. Comparison of miRNAs with the expression of their predicted targets indicated a lower level of concordance than expected. We did, however, find preliminary evidence of combinatorial regulation of mRNA expression by miRNA. The methods described here for comparative analysis of miRNA and mRNA profiling will be useful for better understanding genome wide regulatory responsiveness, and to refine miRNA predictive algorithms under development for that purpose.
Keywords: miRNA, hypoxia, HT29, cystic fibrosis
 
Overall design Two group experiment (noroxia and hypoxia) three replicates per condition
 
Contributor(s) Page GP
Citation(s) 18474670, 19320992
Submission date Oct 04, 2007
Last update date Aug 20, 2019
Contact name Grier Page
E-mail(s) gpage@uab.edu
Phone 205-934-4930
Organization name University of Alabama at Birmingham
Street address
City Birmingham
State/province AL
ZIP/Postal code 35294
Country USA
 
Platforms (2)
GPL570 [HG-U133_Plus_2] Affymetrix Human Genome U133 Plus 2.0 Array
GPL5106 mirVANA miRNA Bioarray V2
Samples (12)
GSM234650 Human normoxia 1 (miRNA array)
GSM234651 Human normoxia 2 (miRNA array)
GSM234652 Human normoxia 3 (miRNA array)
Relations
BioProject PRJNA102837

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE9234_RAW.tar 27.5 Mb (http)(custom) TAR (of CEL, GPR)
Processed data included within Sample table

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